Zuobai Zhang - RankMe

48 papers A* 14A 4Journal 30

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	PerturbDiff: Functional Diffusion for Single-Cell Perturbation Modeling. CoRR Xinyu Yuan, Xixian Liu, Ya Shi Zhang, Zuobai Zhang, Hongyu Guo, Jian Tang
2026	J	`jnl`	Scaling Atomistic Protein Binder Design with Generative Pretraining and Test-Time Compute. CoRR Kieran Didi, Zuobai Zhang, Guoqing Zhou, Danny Reidenbach, Zhonglin Cao, Sooyoung Cha, Tomas Geffner, Christian Dallago, Jian Tang, Michael M. Bronstein, Martin Steinegger, Emine Küçükbenli, Arash Vahdat, Karsten Kreis
2025	J	`jnl`	La-Proteina: Atomistic Protein Generation via Partially Latent Flow Matching. CoRR Tomas Geffner, Kieran Didi, Zhonglin Cao, Danny Reidenbach, Zuobai Zhang, Christian Dallago, Emine Küçükbenli, Karsten Kreis, Arash Vahdat
2025	J	`jnl`	Means of Hitting Times for Random Walks on Graphs: Connections, Computation, and Optimization. ACM Trans. Knowl. Discov. Data Haisong Xia, Wanyue Xu, Zuobai Zhang, Zhongzhi Zhang
2025	A*	`conf`	Proteina: Scaling Flow-based Protein Structure Generative Models. ICLR Tomas Geffner, Kieran Didi, Zuobai Zhang, Danny Reidenbach, Zhonglin Cao, Jason Yim, Mario Geiger, Christian Dallago, Emine Küçükbenli, Arash Vahdat, Karsten Kreis
2025	J	`jnl`	Proteina: Scaling Flow-based Protein Structure Generative Models. CoRR Tomas Geffner, Kieran Didi, Zuobai Zhang, Danny Reidenbach, Zhonglin Cao, Jason Yim, Mario Geiger, Christian Dallago, Emine Küçükbenli, Arash Vahdat, Karsten Kreis
2024	A*	`conf`	Cell ontology guided transcriptome foundation model. NeurIPS Xinyu Yuan, Zhihao Zhan, Zuobai Zhang, Manqi Zhou, Jianan Zhao, Boyu Han, Yue Li, Jian Tang
2024	J	`jnl`	Cell-ontology guided transcriptome foundation model. CoRR Xinyu Yuan, Zhihao Zhan, Zuobai Zhang, Manqi Zhou, Jianan Zhao, Boyu Han, Yue Li, Jian Tang
2024	A*	`conf`	Evaluating Representation Learning on the Protein Structure Universe. ICLR Arian Rokkum Jamasb, Alex Morehead, Chaitanya K. Joshi, Zuobai Zhang, Kieran Didi, Simon V. Mathis, Charles Harris, Jian Tang, Jianlin Cheng, Pietro Lio, Tom L. Blundell
2024	J	`jnl`	Evaluating representation learning on the protein structure universe. CoRR Arian R. Jamasb, Alex Morehead, Chaitanya K. Joshi, Zuobai Zhang, Kieran Didi, Simon V. Mathis, Charles Harris, Jian Tang, Jianlin Cheng, Pietro Lio, Tom L. Blundell
2024	J	`jnl`	Fusing Neural and Physical: Augment Protein Conformation Sampling with Tractable Simulations. CoRR Jiarui Lu, Zuobai Zhang, Bozitao Zhong, Chence Shi, Jian Tang
2024	J	`jnl`	Means of Hitting Times for Random Walks on Graphs: Connections, Computation, and Optimization. CoRR Haisong Xia, Wanyue Xu, Zuobai Zhang, Zhongzhi Zhang
2024	A*	`conf`	Multi-Scale Representation Learning for Protein Fitness Prediction. NeurIPS Zuobai Zhang, Pascal Notin, Yining Huang, Aurélie C. Lozano, Vijil Chenthamarakshan, Debora S. Marks, Payel Das, Jian Tang
2024	J	`jnl`	Multi-Scale Representation Learning for Protein Fitness Prediction. CoRR Zuobai Zhang, Pascal Notin, Yining Huang, Aurélie C. Lozano, Vijil Chenthamarakshan, Debora S. Marks, Payel Das, Jian Tang
2024	J	`jnl`	Opinion dynamics in social networks incorporating higher-order interactions. Data Min. Knowl. Discov. Zuobai Zhang, Wanyue Xu, Zhongzhi Zhang, Guanrong Chen
2024	J	`jnl`	ProtIR: Iterative Refinement between Retrievers and Predictors for Protein Function Annotation. CoRR Zuobai Zhang, Jiarui Lu, Vijil Chenthamarakshan, Aurélie C. Lozano, Payel Das, Jian Tang
2024	A*	`conf`	Str2Str: A Score-based Framework for Zero-shot Protein Conformation Sampling. ICLR Jiarui Lu, Bozitao Zhong, Zuobai Zhang, Jian Tang
2024	J	`jnl`	Structure-Informed Protein Language Model. CoRR Zuobai Zhang, Jiarui Lu, Vijil Chenthamarakshan, Aurélie C. Lozano, Payel Das, Jian Tang
2023	A*	`conf`	DiffPack: A Torsional Diffusion Model for Autoregressive Protein Side-Chain Packing. NeurIPS Yangtian Zhang, Zuobai Zhang, Bozitao Zhong, Sanchit Misra, Jian Tang
2023	J	`jnl`	DiffPack: A Torsional Diffusion Model for Autoregressive Protein Side-Chain Packing. CoRR Yangtian Zhang, Zuobai Zhang, Bozitao Zhong, Sanchit Misra, Jian Tang
2023	J	`jnl`	Enhancing Protein Language Models with Structure-based Encoder and Pre-training. CoRR Zuobai Zhang, Minghao Xu, Vijil Chenthamarakshan, Aurélie C. Lozano, Payel Das, Jian Tang
2023	A*	`conf`	FusionRetro: Molecule Representation Fusion via In-Context Learning for Retrosynthetic Planning. ICML Songtao Liu, Zhengkai Tu, Minkai Xu, Zuobai Zhang, Lu Lin, Rex Ying, Jian Tang, Peilin Zhao, Dinghao Wu
2023	J	`jnl`	PDB-Struct: A Comprehensive Benchmark for Structure-based Protein Design. CoRR Chuanrui Wang, Bozitao Zhong, Zuobai Zhang, Narendra Chaudhary, Sanchit Misra, Jian Tang
2023	J	`jnl`	Physics-Inspired Protein Encoder Pre-Training via Siamese Sequence-Structure Diffusion Trajectory Prediction. CoRR Zuobai Zhang, Minghao Xu, Aurélie C. Lozano, Vijil Chenthamarakshan, Payel Das, Jian Tang
2023	A*	`conf`	Pre-Training Protein Encoder via Siamese Sequence-Structure Diffusion Trajectory Prediction. NeurIPS Zuobai Zhang, Minghao Xu, Aurélie C. Lozano, Vijil Chenthamarakshan, Payel Das, Jian Tang
2023	A*	`conf`	Protein Representation Learning by Geometric Structure Pretraining. ICLR Zuobai Zhang, Minghao Xu, Arian Rokkum Jamasb, Vijil Chenthamarakshan, Aurélie C. Lozano, Payel Das, Jian Tang
2022	J	`jnl`	Biharmonic Distance-Based Performance Metric for Second-Order Noisy Consensus Networks. IEEE Trans. Inf. Theory Yuhao Yi, Bingjia Yang, Zuobai Zhang, Zhongzhi Zhang, Stacy Patterson
2022	J	`jnl`	Coherence Scaling of Noisy Second-Order Scale-Free Consensus Networks. IEEE Trans. Cybern. Wanyue Xu, Bin Wu, Zuobai Zhang, Zhongzhi Zhang, Haibin Kan, Guanrong Chen
2022	A	`conf`	Effects of Stubbornness on Opinion Dynamics. CIKM Wanyue Xu, Liwang Zhu, Jiale Guan, Zuobai Zhang, Zhongzhi Zhang
2022	J	`jnl`	Effects of Stubbornness on Opinion Dynamics. CoRR Wanyue Xu, Liwang Zhu, Jiale Guan, Zuobai Zhang, Zhongzhi Zhang
2022	J	`jnl`	Fast Approximation of Coherence for Second-Order Noisy Consensus Networks. IEEE Trans. Cybern. Zuobai Zhang, Wanyue Xu, Yuhao Yi, Zhongzhi Zhang
2022	J	`jnl`	Metro: Memory-Enhanced Transformer for Retrosynthetic Planning via Reaction Tree. CoRR Songtao Liu, Rex Ying, Zuobai Zhang, Peilin Zhao, Jian Tang, Lu Lin, Dinghao Wu
2022	A*	`conf`	Neural-Symbolic Models for Logical Queries on Knowledge Graphs. ICML Zhaocheng Zhu, Mikhail Galkin, Zuobai Zhang, Jian Tang
2022	J	`jnl`	Neural-Symbolic Models for Logical Queries on Knowledge Graphs. CoRR Zhaocheng Zhu, Mikhail Galkin, Zuobai Zhang, Jian Tang
2022	A*	`conf`	PEER: A Comprehensive and Multi-Task Benchmark for Protein Sequence Understanding. NeurIPS Minghao Xu, Zuobai Zhang, Jiarui Lu, Zhaocheng Zhu, Yangtian Zhang, Chang Ma, Runcheng Liu, Jian Tang
2022	J	`jnl`	PEER: A Comprehensive and Multi-Task Benchmark for Protein Sequence Understanding. CoRR Minghao Xu, Zuobai Zhang, Jiarui Lu, Zhaocheng Zhu, Yangtian Zhang, Chang Ma, Runcheng Liu, Jian Tang
2022	J	`jnl`	Protein Representation Learning by Geometric Structure Pretraining. CoRR Zuobai Zhang, Minghao Xu, Arian R. Jamasb, Vijil Chenthamarakshan, Aurélie C. Lozano, Payel Das, Jian Tang
2022	A	`conf`	Structured Multi-task Learning for Molecular Property Prediction. AISTATS Shengchao Liu, Meng Qu, Zuobai Zhang, Huiyu Cai, Jian Tang
2022	J	`jnl`	Structured Multi-task Learning for Molecular Property Prediction. CoRR Shengchao Liu, Meng Qu, Zuobai Zhang, Huiyu Cai, Jian Tang
2022	J	`jnl`	TorchDrug: A Powerful and Flexible Machine Learning Platform for Drug Discovery. CoRR Zhaocheng Zhu, Chence Shi, Zuobai Zhang, Shengchao Liu, Minghao Xu, Xinyu Yuan, Yangtian Zhang, Jun-Kun Chen, Huiyu Cai, Jiarui Lu, Chang Ma, Runcheng Liu, Louis-Pascal A. C. Xhonneux, Meng Qu, Jian Tang
2021	J	`jnl`	Coherence Scaling of Noisy Second-Order Scale-Free Consensus Networks. CoRR Wanyue Xu, Bin Wu, Zuobai Zhang, Zhongzhi Zhang, Haibin Kan, Guanrong Chen
2021	A	`conf`	Minimizing Spectral Radius of Non-Backtracking Matrix by Edge Removal. CIKM Zuobai Zhang, Zhongzhi Zhang, Guanrong Chen
2021	A*	`conf`	Neural Bellman-Ford Networks: A General Graph Neural Network Framework for Link Prediction. NeurIPS Zhaocheng Zhu, Zuobai Zhang, Louis-Pascal A. C. Xhonneux, Jian Tang
2021	J	`jnl`	Neural Bellman-Ford Networks: A General Graph Neural Network Framework for Link Prediction. CoRR Zhaocheng Zhu, Zuobai Zhang, Louis-Pascal A. C. Xhonneux, Jian Tang
2021	J	`jnl`	Opinion Dynamics Incorporating Higher-Order Interactions. CoRR Zuobai Zhang, Wanyue Xu, Zhongzhi Zhang, Guanrong Chen
2020	A	`conf`	Nearly Linear Time Algorithm for Mean Hitting Times of Random Walks on a Graph. WSDM Zuobai Zhang, Wanyue Xu, Zhongzhi Zhang
2020	A*	`conf`	Opinion Dynamics Incorporating Higher-Order Interactions. ICDM Zuobai Zhang, Wanyue Xu, Zhongzhi Zhang, Guanrong Chen
2020	A*	`conf`	Power-Law Graphs Have Minimal Scaling of Kemeny Constant for Random Walks. WWW Wanyue Xu, Yibin Sheng, Zuobai Zhang, Haibin Kan, Zhongzhi Zhang